Transformer-based convolutional forgetting knowledge tracking.

Knowledge tracking is to analyze the mastery of students' knowledge through the learning track. This is very important for online education, since it can determine a learner's current knowledge level by analyzing the learning history and then make recommendations for future learning. In the past, the commonly used model for knowledge tracking is the convolutional neural network, but it has long-term sequence dependencies. With the invention of Transformer, it has excellent performance in long-sequence modeling by virtue of the attention mechanism, and is gradually introduced into the field of knowledge tracking. However, through our research, some knowledge tracking data sets have a large number of continuous and repetitive training, which will cause Transformer model to ignore the potential connections between some knowledge points. To overcome this problem, we introduce a convolutional attention mechanism to help the model perceive contextual information better. In addition, we simulate the forgetting phenomenon of students during the learning process by calculating the forgetting factor, and fuse it with the weight matrix generated by the model to improve the accuracy of the model. As a result, a Transformer-based Convolutional Forgetting Knowledge Tracking (TCFKT) model is presented in this paper. According to the experimental results conducted on the real world ASSITments2012, ASSISTments2017, KDD a, STATIC datasets, the TCFKT model outperforms other knowledge tracking models.

Identification and Alternative Splicing Profile of the Raffinose synthase Gene in Grass Species.

Raffinose synthase (Rafs) is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and plant responses to abiotic stresses. In this study, we analyzed the Rafs families and profiled their alternative splicing patterns at the genome-wide scale from 10 grass species representing crops and grasses. A total of 73 Rafs genes were identified from grass species such as rice, maize, foxtail millet, and switchgrass. These Rafs genes were assigned to six groups based the phylogenetic analysis. We compared the gene structures, protein domains, and expression patterns of Rafs genes, and also unraveled the alternative transcripts of them. In addition, different conserved sequences were observed at these putative splice sites among grass species. The subcellular localization of PvRafs5 suggested that the Rafs gene was expressed in the cytoplasm or cell membrane. Our findings provide comprehensive knowledge of the Rafs families in terms of genes and proteins, which will facilitate further functional characterization in grass species in response to abiotic stress.

Iterative heterogeneous graph learning for knowledge graph-based recommendation.

Incorporating knowledge graphs into recommendation systems has attracted wide attention in various fields recently. A Knowledge graph contains abundant information with multi-type relations among multi-type nodes. The heterogeneous structure reveals not only the connectivity but also the complementarity between the nodes within a KG, which helps to capture the signal of potential interest of the user. However, existing research works have limited abilities in dealing with the heterogeneous nature of knowledge graphs, resulting in suboptimal recommendation results. In this paper, we propose a new recommendation method based on iterative heterogeneous graph learning on knowledge graphs (HGKR). By treating a knowledge graph as a heterogeneous graph, HGKR achieves more fine-grained modeling of knowledge graphs for recommendation. Specifically, we incorporate the graph neural networks into the message passing and aggregating of entities within a knowledge graph both at the graph and the semantic level. Furthermore, we designed a knowledge-perceiving item filter based on an attention mechanism to capture the user's potential interest in their historical preferences for the enhancement of recommendation. Extensive experiments conducted on two datasets in the context of two recommendations reveal the excellence of our proposed method, which outperforms other benchmark models.

Investigating the dynamics of protein-protein interactions in plants.

Both stable and transient protein interactions play an important role in the complex assemblies required for the proper functioning of living cells. Several methods have been developed to monitor protein-protein interactions in plants. However, the detection of dynamic protein complexes is very challenging, with few technologies available for this purpose. Here, we developed a new platform using the plant UBIQUITIN promoter to drive transgene expression and thereby to detect protein interactions in planta. Typically, to decide which side of the protein to link the tags, the subcellular localization of the protein fused either N-terminal or C-terminal mCitrine was firstly confirmed by using eight different specific mCherry markers. Following stable or transient protein expression in plants, the protein interaction network was detected by affinity purification mass spectrometry. These interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC), bioluminescence resonance energy transfer and co-immunoprecipitation assays. The dynamics of these interactions were monitored by Förster resonance energy transfer (FRET) and split-nano luciferase, whilst the ternary protein complex association was monitored by BiFC-FRET. Using the canonical glycolytic metabolon as an example, the interaction between these enzymes was characterized under conditions that mimic physiologically relevant energy statuses.

Integrated bioinformatic and physiological analyses reveal the pivotal role of hydrogen sulfide in enhancing low-temperature tolerance in alfalfa.

Hydrogen sulfide (H2 S) is an important gaseous signal molecule that regulates plant growth and stress resistance. However, research on the H2 S synthase (HSase) genes is still limited in the model legume plant Medicago truncatula Gaertn. In the present study, a total of 40 HSase family members were first identified and analyzed in the M. truncatula genome, and these genes distributed across eight chromosomes and were clustered into five groups (I-V) based on their conserved gene structures and protein motifs. Expression analysis revealed that the MtHSase genes were expressed in all the tested abiotic stresses, albeit with expression level differences. This study also showed that H2 S improves low temperature tolerance of alfalfa seedlings by regulating the antioxidant defense system and enhancing photosynthetic capacity. Thus, the study provides new insights into how the H2 S signal regulates tolerance to low-temperature stress and provides the basis for further gene function and detection.

Isolation and identification of plant growth-promoting rhizobacteria from tall fescue rhizosphere and their functions under salt stress.

Soil salinity has become one of the major factors that threaten tall fescue growth and turf quality. Plants recruit diverse microorganisms in the rhizosphere to cope with salinity stress. In this study, 15 plant growth-promoting rhizobacteria (PGPR) were isolated from the salt-treated rhizosphere of tall fescue and were annotated to 10 genera, including Agrobacterium, Fictibacillus, Rhizobium, Bhargavaea, Microbacterium, Paenarthrobacter, Pseudarthrobacter, Bacillus, Halomonas, and Paracoccus. All strains could produce indole-3-acetic acid (IAA). Additionally, eight strains exhibited the ability to solubilize phosphate and potassium. Most strains could grow on the medium containing 600 mM NaCl, such as Bacillus zanthoxyli and Bacillus altitudinis. Furthermore, Bacillus zanthoxyli and Bacillus altitudinis were inoculated with tall fescue seeds and seedlings to determine their growth-promoting effect. The results showed that Bacillus altitudinis and mixed culture significantly increased the germination rate of tall fescue seeds. Bacillus zanthoxyli can significantly increase the tillers number and leaf width of seedlings under salt conditions. Through the synergistic effect of FaSOS1, FaHKT1, and FaHAK1 genes, Bacillus zanthoxyli helps to expel the excess Na+ from aboveground parts and absorb more K+ in roots to maintain ion homeostasis in tall fescue. Unexpectedly, we found that Bacillus altitudinis displayed an inapparent growth-promoting effect on seedlings under salt stress. Interestingly, the mixed culture of the two strains was also able to alleviate, to some extent, the effects of salt stress on tall fescue. This study provides a preliminary understanding of tall fescue rhizobacteria and highlights the role of Bacillus zanthoxyli in tall fescue growth and salt tolerance.

5-Aminolevulinic acid promotes low-light tolerance by regulating chloroplast ultrastructure, photosynthesis, and antioxidant capacity in tall fescue.

The vital signaling molecule 5-Aminolevulinic acid (ALA) plays critical roles in signal transduction and biological modulation under abiotic stresses. In this study, we explored the effects of exogenous ALA on low-light (LL) stress-induced photosynthesis and antioxidant system damage in tall fescue (Festuca arundinacea Schreb.) seedlings. LL stress decreased morphological index values and chlorophyll contents, while also reduced net photosynthetic rate (Pn) and the maximum quantum yield of photosystem II photochemistry (Fv/Fm). Notably, these restrictions were substantially alleviated by exogenous ALA. Moreover, the contents of chlorophyll and its synthetic precursors were significantly increased after ALA treatment. Meanwhile, ALA observably enhanced expression level of FaCHLG, FaHEMA, FaPOR, and FaCAO, which encode the chlorophyll precursors biosynthesis enzymes. Exogenous ALA repaired the damage to the chloroplast ultrastructure caused by LL stress and promoted the formation of ordered thylakoids and grana lamella. ALA also improved Rubisco activity and expression level of the photosynthetic enzyme genes FaRuBP, FaPRK, and FaGADPH. Additionally, application of exogenous ALA decreased relative electrolytic leakage and the accumulation of malondialdehyde (MDA), hydrogen peroxide (H2O2), and superoxide radicals (O2∙-), and increased the gene expression levels and activity of antioxidant enzymes. The ratios of ascorbic acid (AsA) to dehydroascorbic acid (DHA) and reduced glutathione (GSH) to oxidized glutathione (GSSG) were also increased significantly by application of ALA. Furthermore, all responses could be reversed by treatment with levulinic acid (LA). Thus, these results indicated that ALA protects tall fescue from LL stress through scavenging ROS, improving photosynthetic enzyme activity levels, increasing photosynthetic pigments contents, repairing chloroplast damage, and enhancing the photosynthesis rate.

Paclobutrazol Ameliorates Low-Light-Induced Damage by Improving Photosynthesis, Antioxidant Defense System, and Regulating Hormone Levels in Tall Fescue.

Paclobutrazol (PBZ) is a plant-growth regulator (PGR) in the triazole family that enhances plant tolerance to environmental stresses. Low-light (LL) intensity is a critical factor adversely affecting the growth of tall fescue (Festuca arundinacea Schreb.). Therefore, in this study, tall fescue seedlings were treated with PBZ under control and LL conditions to investigate the effects of PBZ on enhancing LL stress resistance by regulating the growth, photosynthesis, oxidative defense, and hormone levels. Our results reveal that LL stress reduced the total biomass, chlorophyll (Chl) content, photosynthetic capacity, and photochemical efficiency of photosystem II (PSII) but increased the membrane lipid peroxidation level and reactive oxygen species (ROS) generation. However, the application of PBZ increased the photosynthetic pigment contents, net photosynthetic rate (Pn), maximum quantum yield of PSII photochemistry (Fv/Fm), ribulose-1,5-bisphosphate carboxylase (RuBisCO) activity, and starch content. In addition, PBZ treatment activated the antioxidant enzyme activities, antioxidants contents, ascorbate acid-glutathione (AsA-GSH) cycle, and related gene expression, lessening the ROS burst (H2O2 and O2∙-). However, the gibberellic acid (GA) anabolism was remarkably decreased by PBZ treatment under LL stress, downregulating the transcript levels of kaurene oxidase (KO), kaurenoic acid oxidase (KAO), and GA 20-oxidases (GA20ox). At the same time, PBZ treatment up-regulated 9-cis-epoxycarotenoid dioxygenase (NCED) gene expression, significantly increasing the endogenous abscisic acid (ABA) concentration under LL stress. Thus, our study revealed that PBZ improves the antioxidation and photosynthetic capacity, meanwhile increasing the ABA concentration and decreasing GA concentration, which ultimately enhances the LL stress tolerance in tall fescue.

Hydrogen sulfide improves tall fescue photosynthesis response to low-light stress by regulating chlorophyll and carotenoid metabolisms.

Hydrogen sulfide (H2S), as a gaseous messenger molecule, plays critical roles in signal transduction and biological modulation. In the present study, the roles of H2S in regulating chlorophyll (Chl) and carotenoid (Car) contents to improve photosynthesis in tall fescue were investigated under low-light (LL) stress. Compared to control conditions, LL stress significantly reduced total biomass, net photosynthetic rate (Pn), maximal quantum yield of photosystem II (PSII) photochemistry (Fv/Fm), and the contents of Chl and Car. Under exogenous sodium hydrosulfide (NaHS, H2S donor) application, these parameters were enhanced, ultimately increasing photosynthesis. Moreover, exogenous H2S up-regulated the expression of chlorophyll biosynthesis genes while down-regulated chlorophyll degradation genes, resulting in increases in chlorophyll precursors. Components of carotenoids and expression of genes encoding biosynthesis and degradation enzymes varied similarly. Additionally, application exogenous H2S up-regulated expression of FaDES1 and FaDCD. Thus, it enhanced L-cysteine desulfhydrase 1 (DES1, EC 4.4.1.1) and D-cysteine desulfhydrase (DCD, EC 4.4.1.15) activities leading to elevated endogenous H2S. However, these responses were reversed by treatment with hypotaurine (HT, H2S scavenger). These results suggested that H2S is involved in regulating photosynthesis to improve LL tolerance via modulating Chl and Car metabolisms in tall fescue.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath.

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight.

MAIN CONCLUSION: Rhizosheath comprises soil that adheres firmly to roots. In this study, two ecotypes of switchgrass with different rhizosheath sizes after drought stress were analyzed which showed metabolic differences under drought conditions. The rhizosheath comprises soil that adheres firmly to roots by a combination of root hairs and mucilage and may aid in root growth under soil drying. The aim of this work is to reveal the potential metabolites involved in rhizosheath formation under drought stress conditions. Panicum virgatum L. (switchgrass), which belongs to the Poaceae family, is an important biofuel and fodder crop in drought areas. Five switchgrass ecotypes (cv. Alamo, cv. Blackwake, cv. Summer, cv. Cave-in-Rock and cv. Kanlow) have a broad range of rhizosheath weight under drought conditions. For two selected ecotypes with contrast rhizosheath weight (cv. Alamo and cv. Kanlow), root hair length and density, lateral root number, root morphological parameters were measured, and real-time qRT-PCR was performed. Gas chromatography mass spectrophotometry (GC-MS) was used to determine the primary metabolites in the shoots and roots of selected ecotypes under drought stress conditions. The change trends of root hair length and density, lateral root number and related gene expression were consistent with rhizosheath weight in Alamo and Kanlow under drought and watered conditions. For root morphological parameters, Alamo grew deeper than Kanlow, while Kanlow exhibited higher values for other parameters. In this study, the levels of amino acids, sugars and organic acids were significantly changed in response to drought stress in two switchgrass ecotypes. Several metabolites including amino acids (arginine, isoleucine, methionine and cysteine) and sugars (kestose, raffinose, fructose, fucose, sorbose and xylose) in the large soil-sheathed roots of Alamo and Kanlow were significantly increased compared to small or no soil-sheathed roots of Alamo and Kanlow. Difference in rhizosheath size is reflected in the plant internal metabolites under drought stress conditions. Additionally, our results highlight the importance of using metabolite profiling and provide a better understanding of rhizosheath formation at the cellular level.

Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species.

MAIN CONCLUSION: The work offers a comprehensive evaluation on the phylogenetics and conservation of splicing patterns of the plant SPF30 splicing factor gene family. In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genome-wide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.

Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress.

The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%-14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.

Alternative splicing and translation play important roles in hypoxic germination in rice.

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.

Evolution by duplication: paleopolyploidy events in plants reconstructed by deciphering the evolutionary history of VOZ transcription factors.

BACKGROUND: Facilitated by the rapid progress of sequencing technology, comparative genomic studies in plants have unveiled recurrent whole genome duplication (i.e. polyploidization) events throughout plant evolution. The evolutionary past of plant genes should be analyzed in a background of recurrent polyploidy events in distinctive plant lineages. The Vascular Plant One Zinc-finger (VOZ) gene family encode transcription factors associated with a number of important traits including control of flowering time and photoperiodic pathways, but the evolutionary trajectory of this gene family remains uncharacterized. RESULTS: In this study, we deciphered the evolutionary history of the VOZ gene family by analyses of 107 VOZ genes in 46 plant genomes using integrated methods: phylogenic reconstruction, Ks-based age estimation and genomic synteny comparisons. By scrutinizing the VOZ gene family phylogeny the core eudicot γ event was well circumscribed, and relics of the precommelinid τ duplication event were detected by incorporating genes from oil palm and banana. The more recent T and ρ polyploidy events, closely coincident with the species diversification in Solanaceae and Poaceae, respectively, were also identified. Other important polyploidy events captured included the "salicoid" event in poplar and willow, the "early legume" and "soybean specific" events in soybean, as well as the recent polyploidy event in Physcomitrella patens. Although a small transcription factor gene family, the evolutionary history of VOZ genes provided an outstanding record of polyploidy events in plants. The evolutionary past of VOZ gene family demonstrated a close correlation with critical plant polyploidy events which generated species diversification and provided answer to Darwin's "abominable mystery". CONCLUSIONS: We deciphered the evolutionary history of VOZ transcription factor family in plants and ancestral polyploidy events in plants were recapitulated simultaneously. This analysis allowed for the generation of an idealized plant gene tree demonstrating distinctive retention and fractionation patterns following polyploidy events.

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.

BACKGROUND: The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China's sequencing market, would be a preferable reference to evaluate new platforms. METHODS: To this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms. RESULTS: The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88-0.93) and intra-platform (correlation, 0.95-0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion-deletion analysis. CONCLUSION: The present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis.

Natural variation in the promoter of rice calcineurin B-like protein10 (OsCBL10) affects flooding tolerance during seed germination among rice subspecies.

Rice (Oryza sativa L.) has two ecotypes, upland and lowland rice, that have been observed to show different tolerance levels under flooding stress. In this study, two rice cultivars, upland (Up221, flooding-intolerant) and lowland (Low88, flooding-tolerant), were initially used to study their molecular mechanisms in response to flooding germination. We observed that variations in the OsCBL10 promoter sequences in these two cultivars might contribute to this divergence in flooding tolerance. Further analysis using another eight rice cultivars revealed that the OsCBL10 promoter could be classified as either a flooding-tolerant type (T-type) or a flooding-intolerant type (I-type). The OsCBL10 T-type promoter only existed in japonica lowland cultivars, whereas the OsCBL10 I-type promoter existed in japonica upland, indica upland and indica lowland cultivars. Flooding-tolerant rice cultivars containing the OsCBL10 T-type promoter have shown lower Ca2+ flow and higher α-amylase activities in comparison to those in flooding-intolerant cultivars. Furthermore, the OsCBL10 overexpression lines were sensitive to both flooding and hypoxic treatments during rice germination with enhanced Ca2+ flow in comparison to wild-type. Subsequent findings also indicate that OsCBL10 may affect OsCIPK15 protein abundance and its downstream pathways. In summary, our results suggest that the adaptation to flooding stress during rice germination is associated with two different OsCBL10 promoters, which in turn affect OsCBL10 expression in different cultivars and negatively affect OsCIPK15 protein accumulation and its downstream cascade.

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings.

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.

A Phylogenetically Informed Comparison of GH1 Hydrolases between Arabidopsis and Rice Response to Stressors.

Glycoside hydrolases Family 1 (GH1) comprises enzymes that can hydrolyze ß-O-glycosidic bond from a carbohydrate moiety. The plant GH1 hydrolases participate in a number of developmental processes and stress responses, including cell wall modification, plant hormone activation or deactivation and herbivore resistance. A large number of members has been observed in this family, suggesting their potential redundant functions in various biological processes. In this study, we have used 304 sequences of plant GH1 hydrolases to study the evolution of this gene family in plant lineage. Gene duplication was found to be a common phenomenon in this gene family. Although many members of GH1 hydrolases showed a high degree of similarity in Arabidopsis and rice, they showed substantial tissue specificity and differential responses to various stress treatments. This differential regulation implies each enzyme may play a distinct role in plants. Furthermore, some of salt-responsive Arabidopsis GH1 hydrolases were selected to test their genetic involvement in salt responses. The knockout mutants of AtBGLU1 and AtBGLU19 were observed to be less-sensitive during NaCl treatment in comparison to the wild type seedlings, indicating their participation in salt stress response. In summary, Arabidopsis and rice GH1 glycoside hydrolases showed distinct features in their evolutionary path, transcriptional regulation and genetic functions.

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.

Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.